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v0.1.3: don't use set_threads after reading header
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@brentp brentp released this 26 Feb 17:00
· 66 commits to main since this release
v0.1.3
7a74193

This release fixes a major bug with dense variant files (like spliceAI)

v0.1.3

  • exit with error on multi-allelics (previously, only first allele was used) ( #11)
  • more docs on conf file (thanks @m-pauper)
  • fix compression error for very dense regions (#12)
  • major: fix error when using hts_set_threads more than once and after reading header (#12)

Get Started

To get started, either download the static linux binary here, then chmod +x and execute.

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.3/echtvar \
    && chmod +x ~/bin/echtvar \
   && ~/bin/echtvar -h

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

Contributors

m-pauper
Assets 3
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